5K2M image
Entry Detail
PDB ID:
5K2M
Title:
Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA
Biological Source:
PDB Version:
Deposition Date:
2016-05-19
Release Date:
2016-09-07
Method Details:
Experimental Method:
Resolution:
2.18 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:RimK-related lysine biosynthesis protein
Chain IDs:A, B, C, D, G, H, I, J
Chain Length:273
Number of Molecules:8
Biological Source:Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Polymer Type:polypeptide(L)
Description:Probable lysine biosynthesis protein
Chain IDs:E, F, K, L, M, N
Chain Length:53
Number of Molecules:6
Biological Source:Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
R0K E GLU modified residue
Primary Citation
Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
J. Biol. Chem. 291 21630 21643 (2016)
PMID: 27566549 DOI: 10.1074/jbc.M116.743021

Abstact

We recently discovered a biosynthetic system using a novel amino group carrier protein called LysW for lysine biosynthesis via α-aminoadipate (AAA), and revealed that this system is also utilized in the biosynthesis of arginine by Sulfolobus In the present study, we focused on the biosynthesis of lysine and ornithine in the hyperthermophilic archaeon Thermococcus kodakarensis, and showed that their biosynthesis is accomplished by a single set of metabolic enzymes. We also determined the crystal structure of the LysX family protein from T. kodakarensis, which catalyzes the conjugation of LysW with either AAA or glutamate, in a complex with LysW-γ-AAA. This crystal structure is the first example to show how LysX recognizes AAA as a substrate and provides a structural basis for the bifunctionality of the LysX family protein from T. kodakarensis Based on comparisons with other LysX family proteins, we propose a mechanism for substrate recognition and its relationship with molecular evolution among LysX family proteins, which have different substrate specificities.

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